diff --git a/examples/hello/hdf5Writer/helloHDF5Writer.cpp b/examples/hello/hdf5Writer/helloHDF5Writer.cpp
index f7ffea4e1d9b1a4d03fecaed0acb76351214802d..71caa0d2b898b1d0e6c202bb9a8e22a38df92786 100644
--- a/examples/hello/hdf5Writer/helloHDF5Writer.cpp
+++ b/examples/hello/hdf5Writer/helloHDF5Writer.cpp
@@ -65,8 +65,11 @@ int main(int argc, char *argv[])
intCountDim1 = intDim1 - rank * (intDim1 / size);
}
- std::cout<<" rank="<<rank<<" of "<<size<<", dim1 count: "<<intCountDim1<<", offset: "<<intOffsetDim1<<std::endl;
- std::cout<<" intOffsetDim2="<<intOffsetDim2<<" "<<intDim2<<std::endl;
+ std::cout << " rank=" << rank << " of " << size
+ << ", dim1 count: " << intCountDim1
+ << ", offset: " << intOffsetDim1 << std::endl;
+ std::cout << " intOffsetDim2=" << intOffsetDim2 << " " << intDim2
+ << std::endl;
try
{
// Define variable and local size
@@ -100,60 +103,66 @@ int main(int argc, char *argv[])
throw std::ios_base::failure(
"ERROR: failed to create HDF5 I/O engine at Open\n");
- int ts = 0;
- int totalts = 2;
- while (true) {
- if (rank == 0) {
- std::cout<<" total timesteps: "<<totalts<<" curr: "<<ts<<" th"<<std::endl;
- }
- HDF5Writer->Write(ioMyDoubles, myDoubles.data() +
- doubleVOffset); // Base class Engine
- // own the Write<T>
- // that will call
- // overloaded Write
- // from Derived
- HDF5Writer->Write(ioMyInts,
- myInts.data() + (intOffsetDim1 * intDim2 ));
-
- HDF5Writer->Write(ioMyCFloats, myCFloats.data() + complexOffset);
- HDF5Writer->Write(ioMyCDoubles, myCDoubles.data() + complexOffset);
- HDF5Writer->Write(ioMyCLongDoubles,
- myCLongDoubles.data() + complexOffset);
- ts++;
- if (ts >= totalts) {
- break;
- }
- HDF5Writer->Advance();
- }
- HDF5Writer->Close();
-
- // now read out:
- /*
- HDF5Settings.SetEngine("HDF5Reader");
- std::cout<<"... Testing a copy of test.h5, [test1.h5] , b/c engine does not decrease name count !! "<<std::endl;
- auto HDF5Reader = adios.Open("test1.h5", "r", HDF5Settings);
-
- //int findts = HDF5Reader->getNumTimeSteps();
- //HDF5Reader->InquireVariableDouble("wrongMyDoubles", true);
- HDF5Reader->InquireVariableDouble(ioMyDoubles.m_Name, true);
- */
-/*
- adios::HDF5Reader myReader(adios, "test.h5", "r", MPI_COMM_WORLD, HDF5Settings);
- double values[15];
-
-#ifndef NEVER
- ts = 0;
- while (ts < totalts) {
- myReader.ReadMe(ioMyDoubles, values, H5T_NATIVE_DOUBLE);
- myReader.Advance();
- ts++;
- }
-
-#else
- myReader.ReadMe(ioMyDoubles, values, H5T_NATIVE_DOUBLE);
-#endif
-*/
+ int ts = 0;
+ int totalts = 2;
+ while (true)
+ {
+ if (rank == 0)
+ {
+ std::cout << " total timesteps: " << totalts << " curr: " << ts
+ << " th" << std::endl;
+ }
+ HDF5Writer->Write(ioMyDoubles,
+ myDoubles.data() +
+ doubleVOffset); // Base class Engine
+ // own the Write<T>
+ // that will call
+ // overloaded Write
+ // from Derived
+ HDF5Writer->Write(ioMyInts,
+ myInts.data() + (intOffsetDim1 * intDim2));
+
+ HDF5Writer->Write(ioMyCFloats, myCFloats.data() + complexOffset);
+ HDF5Writer->Write(ioMyCDoubles, myCDoubles.data() + complexOffset);
+ HDF5Writer->Write(ioMyCLongDoubles,
+ myCLongDoubles.data() + complexOffset);
+ ts++;
+ if (ts >= totalts)
+ {
+ break;
+ }
+ HDF5Writer->Advance();
+ }
+ HDF5Writer->Close();
+ // now read out:
+ /*
+ HDF5Settings.SetEngine("HDF5Reader");
+ std::cout<<"... Testing a copy of test.h5, [test1.h5] , b/c engine does
+ not decrease name count !! "<<std::endl;
+ auto HDF5Reader = adios.Open("test1.h5", "r", HDF5Settings);
+
+ //int findts = HDF5Reader->getNumTimeSteps();
+ //HDF5Reader->InquireVariableDouble("wrongMyDoubles", true);
+ HDF5Reader->InquireVariableDouble(ioMyDoubles.m_Name, true);
+ */
+ /*
+ adios::HDF5Reader myReader(adios, "test.h5", "r",
+ MPI_COMM_WORLD, HDF5Settings);
+ double values[15];
+
+ #ifndef NEVER
+ ts = 0;
+ while (ts < totalts) {
+ myReader.ReadMe(ioMyDoubles, values, H5T_NATIVE_DOUBLE);
+ myReader.Advance();
+ ts++;
+ }
+
+ #else
+ myReader.ReadMe(ioMyDoubles, values, H5T_NATIVE_DOUBLE);
+ #endif
+ */
}
catch (std::invalid_argument &e)
{
diff --git a/source/adios2/ADIOS.cpp b/source/adios2/ADIOS.cpp
index b39ebcc397d3ae71718145532630a7b81ee49a84..7144f668bb6ab9851b84f3ff3269c5d72274a3d0 100644
--- a/source/adios2/ADIOS.cpp
+++ b/source/adios2/ADIOS.cpp
@@ -202,7 +202,7 @@ std::shared_ptr<Engine> ADIOS::Open(const std::string &name,
#else
throw std::invalid_argument("ERROR: this version didn't compile with "
"HDF5 library, can't use HDF5\n");
-#endif
+#endif
}
else
{
diff --git a/source/adios2/engine/hdf5/HDF5Common.cpp b/source/adios2/engine/hdf5/HDF5Common.cpp
index 0862a6babc21f8f2d417c01fbb0d9bc6b970e5b6..8753eaad9f85614f77a6071e314d63be5506fd05 100644
--- a/source/adios2/engine/hdf5/HDF5Common.cpp
+++ b/source/adios2/engine/hdf5/HDF5Common.cpp
@@ -17,12 +17,10 @@
namespace adios
{
-#define H5_ERROR std::cout<<"[ADIOS H5 ERROR] "
+#define H5_ERROR std::cout << "[ADIOS H5 ERROR] "
HDF5Common::HDF5Common()
- :_writeMode(false),
- _total_timestep(0),
- _currentTimeStep(0)
+: _writeMode(false), _total_timestep(0), _currentTimeStep(0)
{
DefH5T_COMPLEX_FLOAT = H5Tcreate(H5T_COMPOUND, sizeof(std::complex<float>));
H5Tinsert(DefH5T_COMPLEX_FLOAT, "freal", 0, H5T_NATIVE_FLOAT);
@@ -39,88 +37,95 @@ HDF5Common::HDF5Common()
H5Tcreate(H5T_COMPOUND, sizeof(std::complex<long double>));
H5Tinsert(DefH5T_COMPLEX_LongDOUBLE, "ldouble real", 0, H5T_NATIVE_LDOUBLE);
H5Tinsert(DefH5T_COMPLEX_LongDOUBLE, "ldouble img",
- H5Tget_size(H5T_NATIVE_LDOUBLE), H5T_NATIVE_LDOUBLE);
+ H5Tget_size(H5T_NATIVE_LDOUBLE), H5T_NATIVE_LDOUBLE);
}
-
-void HDF5Common::H5_Init(const std::string name, MPI_Comm m_MPIComm, bool toWrite)
+void HDF5Common::H5_Init(const std::string name, MPI_Comm m_MPIComm,
+ bool toWrite)
{
_writeMode = toWrite;
//
_plist_id = H5Pcreate(H5P_FILE_ACCESS);
-
+
#ifdef ADIOS2_HAVE_MPI
H5Pset_fapl_mpio(_plist_id, m_MPIComm, MPI_INFO_NULL);
-#endif
+#endif
std::string ts0 = "/TimeStep0";
- if (toWrite) {
- /*
- * Create a new file collectively and release property list identifier.
- */
- _file_id = H5Fcreate(name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, _plist_id);
- if (_file_id >= 0)
- {
- _group_id =
- H5Gcreate2(_file_id, ts0.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
- }
- } else {
- // read a file collectively
- _file_id = H5Fopen(name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
- if (_file_id >= 0)
- {
- _group_id = H5Gopen(_file_id, ts0.c_str(), H5P_DEFAULT);
- }
+ if (toWrite)
+ {
+ /*
+ * Create a new file collectively and release property list identifier.
+ */
+ _file_id =
+ H5Fcreate(name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, _plist_id);
+ if (_file_id >= 0)
+ {
+ _group_id = H5Gcreate2(_file_id, ts0.c_str(), H5P_DEFAULT,
+ H5P_DEFAULT, H5P_DEFAULT);
+ }
+ }
+ else
+ {
+ // read a file collectively
+ _file_id = H5Fopen(name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+ if (_file_id >= 0)
+ {
+ _group_id = H5Gopen(_file_id, ts0.c_str(), H5P_DEFAULT);
+ }
}
H5Pclose(_plist_id);
}
-
+
HDF5Common::~HDF5Common() {}
void HDF5Common::WriteTimeSteps()
{
- if (_file_id < 0)
- {
- //std::cerr<<"[ADIOS HDF5Error]: Invalid file to record timestep to."<<std::endl;
- H5_ERROR<<"Invalid file to record timestep to."<<std::endl;
- return;
- }
+ if (_file_id < 0)
+ {
+ // std::cerr<<"[ADIOS HDF5Error]: Invalid file to record timestep
+ // to."<<std::endl;
+ H5_ERROR << "Invalid file to record timestep to." << std::endl;
+ return;
+ }
- hid_t s = H5Screate(H5S_SCALAR);
+ hid_t s = H5Screate(H5S_SCALAR);
- hid_t attr = H5Acreate(_file_id, "NumTimeSteps", H5T_NATIVE_UINT, s, H5P_DEFAULT, H5P_DEFAULT);
- uint totalts = _currentTimeStep+1;
- H5Awrite(attr,H5T_NATIVE_UINT,&totalts);
+ hid_t attr = H5Acreate(_file_id, "NumTimeSteps", H5T_NATIVE_UINT, s,
+ H5P_DEFAULT, H5P_DEFAULT);
+ uint totalts = _currentTimeStep + 1;
+ H5Awrite(attr, H5T_NATIVE_UINT, &totalts);
- H5Sclose(s);
- H5Aclose(attr);
+ H5Sclose(s);
+ H5Aclose(attr);
}
-
int HDF5Common::GetNumTimeSteps()
{
- if (_file_id < 0)
- {
- std::cerr<<"[ADIOS HDF5Error]: Invalid file to read timestep attribute."<<std::endl;
- return -1;
- }
-
- if (_total_timestep <= 0) {
- hid_t attr = H5Aopen(_file_id, "NumTimeSteps", H5P_DEFAULT);
-
- H5Aread(attr,H5T_NATIVE_UINT, &_total_timestep);
- H5Aclose(attr);
- }
+ if (_file_id < 0)
+ {
+ std::cerr
+ << "[ADIOS HDF5Error]: Invalid file to read timestep attribute."
+ << std::endl;
+ return -1;
+ }
- return _total_timestep;
-}
+ if (_total_timestep <= 0)
+ {
+ hid_t attr = H5Aopen(_file_id, "NumTimeSteps", H5P_DEFAULT);
+ H5Aread(attr, H5T_NATIVE_UINT, &_total_timestep);
+ H5Aclose(attr);
+ }
+ return _total_timestep;
+}
-void HDF5Common::H5_Close() {
+void HDF5Common::H5_Close()
+{
WriteTimeSteps();
H5Gclose(_group_id);
@@ -129,28 +134,28 @@ void HDF5Common::H5_Close() {
void HDF5Common::H5_Advance(int totalts)
{
- _currentTimeStep++;
- if (_currentTimeStep > 0) {
- H5Gclose(_group_id);
- }
+ _currentTimeStep++;
+ if (_currentTimeStep > 0)
+ {
+ H5Gclose(_group_id);
+ }
- std::string tsname="/TimeStep";
- tsname.append(std::to_string(_currentTimeStep));
+ std::string tsname = "/TimeStep";
+ tsname.append(std::to_string(_currentTimeStep));
- if (_writeMode) {
- _group_id =
- H5Gcreate2(_file_id, tsname.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
- } else {
- if ((totalts > 0) && (totalts <= _currentTimeStep))
+ if (_writeMode)
+ {
+ _group_id = H5Gcreate2(_file_id, tsname.c_str(), H5P_DEFAULT,
+ H5P_DEFAULT, H5P_DEFAULT);
+ }
+ else
{
- return;
+ if ((totalts > 0) && (totalts <= _currentTimeStep))
+ {
+ return;
+ }
+ // std::cout<<" ... current group "<<tsname.c_str()<<std::endl;
+ _group_id = H5Gopen(_file_id, tsname.c_str(), H5P_DEFAULT);
}
- //std::cout<<" ... current group "<<tsname.c_str()<<std::endl;
- _group_id =
- H5Gopen(_file_id, tsname.c_str(), H5P_DEFAULT);
- }
}
-
-
-
}
diff --git a/source/adios2/engine/hdf5/HDF5Common.h b/source/adios2/engine/hdf5/HDF5Common.h
index d12994c1cdb24a08ee3c9741c007527812e91bc4..df0c173e4478e6e1cfb196b292a0032df84aa44b 100644
--- a/source/adios2/engine/hdf5/HDF5Common.h
+++ b/source/adios2/engine/hdf5/HDF5Common.h
@@ -11,23 +11,23 @@
#ifndef HDF5_COMMON_P_H_
#define HDF5_COMMON_P_H_
-#include "adios2/core/Engine.h"
#include "adios2/ADIOSMPICommOnly.h"
+#include "adios2/core/Engine.h"
#include <hdf5.h>
namespace adios
{
-class HDF5Common
+class HDF5Common
{
public:
/**
- * Constructor for HDF5 file
+ * Constructor for HDF5 file
* @param file name
*/
- HDF5Common();
+ HDF5Common();
virtual ~HDF5Common();
@@ -35,19 +35,20 @@ public:
void H5_Close();
void H5_Advance(int totalts);
- int GetNumTimeSteps();
+ int GetNumTimeSteps();
void WriteTimeSteps();
- hid_t _plist_id, _file_id;
+ hid_t _plist_id, _file_id;
hid_t _group_id;
-
+
hid_t DefH5T_COMPLEX_DOUBLE;
hid_t DefH5T_COMPLEX_FLOAT;
hid_t DefH5T_COMPLEX_LongDOUBLE;
- int _currentTimeStep;
- private:
- void H5_AdvanceWrite();
+ int _currentTimeStep;
+
+private:
+ void H5_AdvanceWrite();
bool _writeMode;
int _total_timestep;
};
diff --git a/source/adios2/engine/hdf5/HDF5ReaderP.cpp b/source/adios2/engine/hdf5/HDF5ReaderP.cpp
index 9aa7f7b76fb89c95cedbe0efd9656ea263e97352..a70a3c79ca0b72b7964526f11ae6a3ca669ed917 100644
--- a/source/adios2/engine/hdf5/HDF5ReaderP.cpp
+++ b/source/adios2/engine/hdf5/HDF5ReaderP.cpp
@@ -18,21 +18,19 @@ namespace adios
HDF5Reader::HDF5Reader(ADIOS &adios, const std::string name,
const std::string accessMode, MPI_Comm mpiComm,
const Method &method)
-: Engine(adios, "HDF5Reader", name, accessMode, mpiComm,
- method,
+: Engine(adios, "HDF5Reader", name, accessMode, mpiComm, method,
" HDF5Reader constructor (or call to ADIOS Open).\n")
{
- Init();
- MPI_Comm_rank(mpiComm, &_mpi_rank);
- MPI_Comm_size(mpiComm, &_mpi_size);
-
+ Init();
+ MPI_Comm_rank(mpiComm, &_mpi_rank);
+ MPI_Comm_size(mpiComm, &_mpi_size);
}
HDF5Reader::~HDF5Reader() {}
void HDF5Reader::Init()
{
- if (m_AccessMode != "r" && m_AccessMode != "read")
+ if (m_AccessMode != "r" && m_AccessMode != "read")
{
throw std::invalid_argument(
"ERROR: HDF5Reader doesn't support access mode " + m_AccessMode +
@@ -43,231 +41,268 @@ void HDF5Reader::Init()
_H5File.GetNumTimeSteps();
}
-
-Variable<void> * HDF5Reader::InquireVariable(const std::string &variableName,
- const bool readIn )
+Variable<void> *HDF5Reader::InquireVariable(const std::string &variableName,
+ const bool readIn)
{
- std::cout<<"Not implemented: HDF5Reder::InquireVariable()"<<std::endl;
+ std::cout << "Not implemented: HDF5Reder::InquireVariable()" << std::endl;
}
-Variable<char> * HDF5Reader::InquireVariableChar(const std::string &variableName,
- const bool readIn )
-{}
-
-Variable<unsigned char> * HDF5Reader::InquireVariableUChar(const std::string &variableName,
- const bool readIn )
-{}
-
-Variable<short> * HDF5Reader::InquireVariableShort(const std::string &variableName,
- const bool readIn )
-{}
+Variable<char> *HDF5Reader::InquireVariableChar(const std::string &variableName,
+ const bool readIn)
+{
+}
-Variable<unsigned short> * HDF5Reader::InquireVariableUShort(const std::string &variableName,
- const bool readIn)
-{}
+Variable<unsigned char> *
+HDF5Reader::InquireVariableUChar(const std::string &variableName,
+ const bool readIn)
+{
+}
+Variable<short> *
+HDF5Reader::InquireVariableShort(const std::string &variableName,
+ const bool readIn)
+{
+}
+Variable<unsigned short> *
+HDF5Reader::InquireVariableUShort(const std::string &variableName,
+ const bool readIn)
+{
+}
Variable<int> *HDF5Reader::InquireVariableInt(const std::string &variableName,
- const bool)
-{}
+ const bool)
+{
+}
-Variable<unsigned int> *HDF5Reader::InquireVariableUInt(const std::string &variableName,
- const bool)
-{}
+Variable<unsigned int> *
+HDF5Reader::InquireVariableUInt(const std::string &variableName, const bool)
+{
+}
-Variable<long int> *HDF5Reader::InquireVariableLInt(const std::string &variableName,
- const bool)
-{}
+Variable<long int> *
+HDF5Reader::InquireVariableLInt(const std::string &variableName, const bool)
+{
+}
Variable<unsigned long int> *
-HDF5Reader::InquireVariableULInt(const std::string &variableName,
- const bool)
-{}
+HDF5Reader::InquireVariableULInt(const std::string &variableName, const bool)
+{
+}
Variable<long long int> *
-HDF5Reader::InquireVariableLLInt(const std::string &variableName,
- const bool)
-{}
+HDF5Reader::InquireVariableLLInt(const std::string &variableName, const bool)
+{
+}
-Variable<unsigned long long int> *
-HDF5Reader::InquireVariableULLInt(const std::string &variableName,
- const bool)
-{}
+Variable<unsigned long long int> *
+HDF5Reader::InquireVariableULLInt(const std::string &variableName, const bool)
+{
+}
-Variable<float> *HDF5Reader::InquireVariableFloat(const std::string &variableName,
- const bool)
-{}
+Variable<float> *
+HDF5Reader::InquireVariableFloat(const std::string &variableName, const bool)
+{
+}
-Variable<double> *HDF5Reader::InquireVariableDouble(const std::string &variableName,
- const bool)
+Variable<double> *
+HDF5Reader::InquireVariableDouble(const std::string &variableName, const bool)
{
-
- if (_mpi_rank == 0) {
- std::cout<<" ... reading var: "<<variableName<<std::endl;
- }
- int totalts = _H5File.GetNumTimeSteps();
-
- if (_mpi_rank == 0) {
- std::cout<<" ... I saw total timesteps: "<<totalts<<std::endl;
- }
-
- while (true) {
- double values[1];
- UseHDFRead(variableName, values, H5T_NATIVE_DOUBLE);
- Variable<double> v = m_ADIOS.DefineVariable<double>("junk", adios::Dims{8});
- ReadMe(v, values, H5T_NATIVE_DOUBLE);
- if (_H5File._currentTimeStep >= totalts-1) {
- break;
+
+ if (_mpi_rank == 0)
+ {
+ std::cout << " ... reading var: " << variableName << std::endl;
+ }
+ int totalts = _H5File.GetNumTimeSteps();
+
+ if (_mpi_rank == 0)
+ {
+ std::cout << " ... I saw total timesteps: " << totalts << std::endl;
+ }
+
+ while (true)
+ {
+ double values[1];
+ UseHDFRead(variableName, values, H5T_NATIVE_DOUBLE);
+ Variable<double> v =
+ m_ADIOS.DefineVariable<double>("junk", adios::Dims{8});
+ ReadMe(v, values, H5T_NATIVE_DOUBLE);
+ if (_H5File._currentTimeStep >= totalts - 1)
+ {
+ break;
+ }
+ _H5File.H5_Advance(totalts);
}
- _H5File.H5_Advance(totalts);
- }
}
-Variable<long double> * HDF5Reader::InquireVariableLDouble(const std::string &variableName,
- const bool)
-{}
+Variable<long double> *
+HDF5Reader::InquireVariableLDouble(const std::string &variableName, const bool)
+{
+}
-Variable<std::complex<float>> * HDF5Reader::InquireVariableCFloat(const std::string &variableName,
- const bool)
-{}
+Variable<std::complex<float>> *
+HDF5Reader::InquireVariableCFloat(const std::string &variableName, const bool)
+{
+}
-Variable<std::complex<double>> * HDF5Reader::InquireVariableCDouble(const std::string &variableName,
- const bool)
-{}
+Variable<std::complex<double>> *
+HDF5Reader::InquireVariableCDouble(const std::string &variableName, const bool)
+{
+}
-Variable<std::complex<long double>>* HDF5Reader::InquireVariableCLDouble(const std::string &variableName,
- const bool)
-{}
+Variable<std::complex<long double>> *
+HDF5Reader::InquireVariableCLDouble(const std::string &variableName, const bool)
+{
+}
-VariableCompound * HDF5Reader::InquireVariableCompound(const std::string &variableName,
- const bool readIn)
-{}
+VariableCompound *
+HDF5Reader::InquireVariableCompound(const std::string &variableName,
+ const bool readIn)
+{
+}
template <class T>
void HDF5Reader::ReadMe(Variable<T> variable, T *data_array, hid_t h5type)
{
- hid_t datasetID = H5Dopen(_H5File._group_id, variable.m_Name.c_str(), H5P_DEFAULT);
+ hid_t datasetID =
+ H5Dopen(_H5File._group_id, variable.m_Name.c_str(), H5P_DEFAULT);
- if (_mpi_rank == 0) {
- std::cout<<" hdf5 reading variable: "<<variable.m_Name<<" timestep: "<<_H5File._currentTimeStep<<std::endl;
- }
-
- if (datasetID < 0) {
- return;
- }
+ if (_mpi_rank == 0)
+ {
+ std::cout << " hdf5 reading variable: " << variable.m_Name
+ << " timestep: " << _H5File._currentTimeStep << std::endl;
+ }
- hid_t filespace = H5Dget_space(datasetID);
+ if (datasetID < 0)
+ {
+ return;
+ }
- if (filespace < 0) {
- return;
- }
+ hid_t filespace = H5Dget_space(datasetID);
- int ndims = variable.m_GlobalDimensions.size();
- std::vector<hsize_t> count, offset, stride;
+ if (filespace < 0)
+ {
+ return;
+ }
- int elementsRead = 1;
- for (int i = 0; i < ndims; i++)
+ int ndims = variable.m_GlobalDimensions.size();
+ std::vector<hsize_t> count, offset, stride;
+
+ int elementsRead = 1;
+ for (int i = 0; i < ndims; i++)
{
- count.push_back(variable.m_LocalDimensions[i]);
- offset.push_back(variable.m_Offsets[i]);
- stride.push_back(1);
- elementsRead *= variable.m_LocalDimensions[i];
+ count.push_back(variable.m_LocalDimensions[i]);
+ offset.push_back(variable.m_Offsets[i]);
+ stride.push_back(1);
+ elementsRead *= variable.m_LocalDimensions[i];
}
- hid_t ret=H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset.data(), stride.data(), count.data(), NULL);
- if (ret < 0) {
- return;
- }
+ hid_t ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset.data(),
+ stride.data(), count.data(), NULL);
+ if (ret < 0)
+ {
+ return;
+ }
- hid_t mem_dataspace = H5Screate_simple (ndims, count.data(), NULL);
+ hid_t mem_dataspace = H5Screate_simple(ndims, count.data(), NULL);
- //T data_array[elementsRead];
- ret = H5Dread(datasetID, h5type, mem_dataspace, filespace, H5P_DEFAULT, data_array);
+ // T data_array[elementsRead];
+ ret = H5Dread(datasetID, h5type, mem_dataspace, filespace, H5P_DEFAULT,
+ data_array);
- for (int i=0; i<elementsRead; i++) {
- std::cout<<"... ts "<<_H5File._currentTimeStep<<", "<<data_array[i]<<std::endl;
- }
+ for (int i = 0; i < elementsRead; i++)
+ {
+ std::cout << "... ts " << _H5File._currentTimeStep << ", "
+ << data_array[i] << std::endl;
+ }
- H5Sclose(mem_dataspace);
+ H5Sclose(mem_dataspace);
- H5Sclose(filespace);
- H5Dclose(datasetID);
+ H5Sclose(filespace);
+ H5Dclose(datasetID);
}
-
-
-template<class T>
-void HDF5Reader::UseHDFRead(const std::string& variableName, T* values, hid_t h5type)
+template <class T>
+void HDF5Reader::UseHDFRead(const std::string &variableName, T *values,
+ hid_t h5type)
{
- hid_t datasetID = H5Dopen(_H5File._group_id, variableName.c_str(), H5P_DEFAULT);
- if (_mpi_rank == 0) {
- std::cout<<" opened to read: "<<variableName<<std::endl;
- }
-
- if (datasetID < 0) {
- return;
- }
- hid_t filespace = H5Dget_space(datasetID);
-
- if (filespace < 0) {
- return;
- }
- int ndims = H5Sget_simple_extent_ndims(filespace);
- hsize_t dims[ndims];
- herr_t status_n = H5Sget_simple_extent_dims(filespace, dims, NULL);
-
- hsize_t start[ndims]={0}, count[ndims]={0}, stride[ndims]={1};
-
- int totalElements = 1;
- for (int i=0; i<ndims; i++) {
- std::cout<<" ["<<i<<"] th dimension: "<<dims[i]<<std::endl;
- count[i] = dims[i];
- totalElements *= dims[i];
- }
-
- start[0] = _mpi_rank * dims[0]/_mpi_size;
- count[0] = dims[0]/_mpi_size;
- if (_mpi_rank == _mpi_size -1) {
- count[0] = dims[0] - count[0]*(_mpi_size - 1);
- std::cout<<" rank = "<<_mpi_rank<<", count="<<count[0]<<std::endl;
- }
-
- hid_t ret=H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, NULL);
- if (ret < 0) {
- return;
- }
-
- hid_t mem_dataspace = H5Screate_simple (ndims, count, NULL);
-
- int elementsRead = 1;
- for (int i=0; i<ndims; i++) {
- elementsRead *= count[i];
- }
-
- T data_array[elementsRead];
- ret = H5Dread(datasetID, h5type, mem_dataspace, filespace, H5P_DEFAULT, data_array);
-
- for (int i=0; i<elementsRead; i++) {
- std::cout<<"... rank "<<_mpi_rank<<" , "<<data_array[i]<<std::endl;
- }
-
- H5Sclose(mem_dataspace);
-
- H5Sclose(filespace);
- H5Dclose(datasetID);
+ hid_t datasetID =
+ H5Dopen(_H5File._group_id, variableName.c_str(), H5P_DEFAULT);
+ if (_mpi_rank == 0)
+ {
+ std::cout << " opened to read: " << variableName << std::endl;
+ }
+
+ if (datasetID < 0)
+ {
+ return;
+ }
+ hid_t filespace = H5Dget_space(datasetID);
+
+ if (filespace < 0)
+ {
+ return;
+ }
+ int ndims = H5Sget_simple_extent_ndims(filespace);
+ hsize_t dims[ndims];
+ herr_t status_n = H5Sget_simple_extent_dims(filespace, dims, NULL);
+
+ hsize_t start[ndims] = {0}, count[ndims] = {0}, stride[ndims] = {1};
+
+ int totalElements = 1;
+ for (int i = 0; i < ndims; i++)
+ {
+ std::cout << " [" << i << "] th dimension: " << dims[i] << std::endl;
+ count[i] = dims[i];
+ totalElements *= dims[i];
+ }
+
+ start[0] = _mpi_rank * dims[0] / _mpi_size;
+ count[0] = dims[0] / _mpi_size;
+ if (_mpi_rank == _mpi_size - 1)
+ {
+ count[0] = dims[0] - count[0] * (_mpi_size - 1);
+ std::cout << " rank = " << _mpi_rank << ", count=" << count[0]
+ << std::endl;
+ }
+
+ hid_t ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride,
+ count, NULL);
+ if (ret < 0)
+ {
+ return;
+ }
+
+ hid_t mem_dataspace = H5Screate_simple(ndims, count, NULL);
+
+ int elementsRead = 1;
+ for (int i = 0; i < ndims; i++)
+ {
+ elementsRead *= count[i];
+ }
+
+ T data_array[elementsRead];
+ ret = H5Dread(datasetID, h5type, mem_dataspace, filespace, H5P_DEFAULT,
+ data_array);
+
+ for (int i = 0; i < elementsRead; i++)
+ {
+ std::cout << "... rank " << _mpi_rank << " , " << data_array[i]
+ << std::endl;
+ }
+
+ H5Sclose(mem_dataspace);
+
+ H5Sclose(filespace);
+ H5Dclose(datasetID);
}
-
void HDF5Reader::Advance(float timeout_sec)
{
- int totalts = _H5File.GetNumTimeSteps();
- _H5File.H5_Advance(totalts);
+ int totalts = _H5File.GetNumTimeSteps();
+ _H5File.H5_Advance(totalts);
}
-void HDF5Reader::Close(const int transportIndex)
-{
- _H5File.H5_Close();
-}
+void HDF5Reader::Close(const int transportIndex) { _H5File.H5_Close(); }
} // end namespace adios
diff --git a/source/adios2/engine/hdf5/HDF5ReaderP.h b/source/adios2/engine/hdf5/HDF5ReaderP.h
index 5298be8f65681a18bf4978c4ad6851bd07e84888..d1ed06863ab80d29cbf5555bfccebffa099ac80b 100644
--- a/source/adios2/engine/hdf5/HDF5ReaderP.h
+++ b/source/adios2/engine/hdf5/HDF5ReaderP.h
@@ -13,8 +13,8 @@
#include "HDF5Common.h"
-#include "adios2/core/Engine.h"
#include "adios2/ADIOSMPICommOnly.h"
+#include "adios2/core/Engine.h"
namespace adios
{
@@ -24,15 +24,15 @@ class HDF5Reader : public Engine
public:
/**
- * Constructor for single HDF5 reader engine, reads from HDF5 format
+ * Constructor for single HDF5 reader engine, reads from HDF5 format
* @param name unique name given to the engine
* @param accessMode
* @param mpiComm
* @param method
*/
HDF5Reader(ADIOS &adios, const std::string name,
- const std::string accessMode, MPI_Comm mpiComm,
- const Method &method);
+ const std::string accessMode, MPI_Comm mpiComm,
+ const Method &method);
virtual ~HDF5Reader();
@@ -40,7 +40,7 @@ public:
const bool readIn = true);
Variable<char> *InquireVariableChar(const std::string &variableName,
- const bool readIn = true);
+ const bool readIn = true);
Variable<unsigned char> *
InquireVariableUChar(const std::string &variableName,
@@ -108,13 +108,11 @@ public:
void Close(const int transportIndex = -1);
-
template <class T>
- void UseHDFRead(const std::string& variableName, T *values, hid_t h5type);
-
- template <class T>
- void ReadMe(Variable<T> variable, T *values, hid_t h5type);
+ void UseHDFRead(const std::string &variableName, T *values, hid_t h5type);
+ template <class T>
+ void ReadMe(Variable<T> variable, T *values, hid_t h5type);
private:
HDF5Common _H5File;
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.cpp b/source/adios2/engine/hdf5/HDF5WriterP.cpp
index befa9e1a9bea637a0ccd253ec486bad200428949..18aeb1a0d6cdf498965a99a6d1425cb227e2fdab 100644
--- a/source/adios2/engine/hdf5/HDF5WriterP.cpp
+++ b/source/adios2/engine/hdf5/HDF5WriterP.cpp
@@ -25,7 +25,7 @@ HDF5Writer::HDF5Writer(ADIOS &adios, const std::string name,
" HDF5Writer constructor (or call to ADIOS Open).\n"),
m_Buffer(m_DebugMode)
{
- Init();
+ Init();
}
HDF5Writer::~HDF5Writer() {}
@@ -239,26 +239,25 @@ void HDF5Writer::Write(const std::string variableName,
values, _H5File.DefH5T_COMPLEX_LongDOUBLE);
}
-void HDF5Writer::Advance(float timeout_sec)
-{
- _H5File.H5_Advance(0);
-}
+void HDF5Writer::Advance(float timeout_sec) { _H5File.H5_Advance(0); }
void HDF5Writer::Close(const int transportIndex)
{
- /*
- //void* hi = H5Iobject_verify(H5S_SCALAR, H5I_DATASPACE);
-
- hid_t s = H5Screate(H5S_SCALAR);
- //hid_t attr = H5Acreate(_H5File._group_id, "NumTimeSteps", H5T_NATIVE_UINT, s, H5P_DEFAULT, H5P_DEFAULT);
- hid_t attr = H5Acreate(_H5File._file_id, "NumTimeSteps", H5T_NATIVE_UINT, s, H5P_DEFAULT, H5P_DEFAULT);
- uint totalts = _H5File._currentTimeStep+1;
- H5Awrite(attr,H5T_NATIVE_UINT,&totalts);
-
- H5Sclose(s);
- H5Aclose(attr);
- */
- _H5File.H5_Close();
+ /*
+ //void* hi = H5Iobject_verify(H5S_SCALAR, H5I_DATASPACE);
+
+ hid_t s = H5Screate(H5S_SCALAR);
+ //hid_t attr = H5Acreate(_H5File._group_id, "NumTimeSteps", H5T_NATIVE_UINT,
+ s, H5P_DEFAULT, H5P_DEFAULT);
+ hid_t attr = H5Acreate(_H5File._file_id, "NumTimeSteps", H5T_NATIVE_UINT, s,
+ H5P_DEFAULT, H5P_DEFAULT);
+ uint totalts = _H5File._currentTimeStep+1;
+ H5Awrite(attr,H5T_NATIVE_UINT,&totalts);
+
+ H5Sclose(s);
+ H5Aclose(attr);
+ */
+ _H5File.H5_Close();
}
template <class T>
@@ -294,8 +293,9 @@ void HDF5Writer::UseHDFWrite(Variable<T> &variable, const T *values,
hid_t _filespace = H5Screate_simple(dimSize, dimsf.data(), NULL);
- hid_t _dset_id = H5Dcreate(_H5File._group_id, variable.m_Name.c_str(), h5type, _filespace,
- H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ hid_t _dset_id =
+ H5Dcreate(_H5File._group_id, variable.m_Name.c_str(), h5type,
+ _filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
// H5Sclose(_filespace);
hid_t _memspace = H5Screate_simple(dimSize, count.data(), NULL);
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.h b/source/adios2/engine/hdf5/HDF5WriterP.h
index 6dd5c697249f8f6369d7bf735c39717ef7909192..3141cca753a27f7060c343f9f034c3f0a0d9fe51 100644
--- a/source/adios2/engine/hdf5/HDF5WriterP.h
+++ b/source/adios2/engine/hdf5/HDF5WriterP.h
@@ -29,7 +29,7 @@ class HDF5Writer : public Engine
public:
/**
- * Constructor for HDF5 writer engine, writes in hdf5 format
+ * Constructor for HDF5 writer engine, writes in hdf5 format
* @param name unique name given to the engine
* @param accessMode
* @param mpiComm
@@ -94,7 +94,7 @@ private:
capsule::STLVector m_Buffer;
void Init();
-
+
HDF5Common _H5File;
/*
@@ -102,11 +102,11 @@ private:
hid_t _memspace, _filespace;
hid_t _group_id;
-
+
hid_t DefH5T_COMPLEX_DOUBLE;
hid_t DefH5T_COMPLEX_FLOAT;
hid_t DefH5T_COMPLEX_LongDOUBLE;
-
+
int _currentTimeStep;
*/
template <class T>